Wednesday, March 10, 2010

Spiral Motion of Proteins Along DNA

When the great chemist Linus Pauling guessed at the DNA molecular structure he envisioned the bases to be pointing outward rather than being neatly stacked within the double helix as we know them to be. One virtue of Pauling's design is that the information-bearing bases are easily accessible. As it is, the DNA molecule must be unwound and the two strands separated when a gene is transcribed. And even before this happens the protein machines, that do the unwinding and other functions, need to determine where to go on the long DNA double helix. They do so very quickly, but how?

The protein machines that work on the DNA molecule find their starting location quickly. This means they must not be searching randomly within the cell, but instead must be intelligently moving along the DNA.

But do they actually spiral around the DNA in the grooves of the double helix molecule? New research indicates that they do, even though such a spiraling action has considerably more resistance than a non rotating motion would have. This means the the rate at which these proteins slide along the DNA is quite sensitive to the protein size, and therefore controllable by adjusting the protein size.

16 comments:

"need to determine where to go" "This means they must not be searching randomly within the cell, but instead must be intelligently moving along the DNA."

Determine, intelligently moving?

Although coupled, the proteins are still 'finding' their targets by linear diffusion-a random process. If I drove to work with a car whose motion was controlled by a molecule taking a 1-d walk, I'd be arrested.

I suppose you'll just restate the nice evolutionary prediction of the paper--that molecules that must diffuse rapidly along DNA must have have evolved with a small retarding factor--as a design inference. Of course, this restatement is non-falsifiable (unlike the original, which is falsifiable by a single protein that has a large retarding factor and diffused rapidly*) and if I protest, I'll be accused of making a religious slander against the designer.

If possible, I like to look at the original. Here...http://www.people.fas.harvard.edu/~skou/papers/helicalDiff-NSMB.pdf

"Because of the strong dependence of the diffusion constant on ε, proteins whose cellular function depends on fast sliding have evolved to minimize ε. The remaining small yet statistically significant differences among the calculated ε values within this diverse set of proteins reflect the differing physical and functional constraints under which each protein’s sliding activity has evolved."

and here...

We have shown that nonspecifically bound protein molecules diffuse along the helical path defined by DNA and rotate in order to keep the DNA-binding face of the protein in contact with DNA during fast 1D sliding along DNA. Obligate tracking of the DNA helix by sliding protein molecules, and the accompanying 360-degree rotation per helical turn, are prerequisites for efficient recognition of targets in DNA3,16 and are necessary for the conveyance of some types of information by proteins along DNA, as recently proposed for the type III restriction enzymes24. For each protein type, a particular helical track along the DNA represents a locus of low free-energy nonspecific binding states that support rapid sliding along the rugged free energy landscape with small barriers along the DNA. By maintaining the protein position and orientation with respect to targeted base pairs, the protein–DNA complex is able to retain a kinetically efficient target-recognizing configuration while rapidly scanning a DNA substrate."

Yes, this seems like a very complicated "design" to have evolved via randomness alone.

However, that is just as metaphysical as suggesting God wouldn't do it this way.

I continue to be impressed which the repetative use of database-like search applications at the DNA level. Normally, I would point out quantum computations are efficient at searches, but this case seems to be a linear search.

Can anyone, in layman's terms, explain how the test for protein–DNA matching can be this fast? I find it difficult to picture this as someone trying a key on one millions of locks to find which one it opens.

In layman's terms, it is really fast diffusion, made faster by limiting it in dimension through non-specific binding to DNA.

This allows rates of scanning of around 4 X 10^6 DNA basepairs/second (for say, a lac repressor). Once a specific target is found, a slower process of specific binding, often with conformational changes occurs. On rates for that step are usually more like seconds.

Now that might work for bacteria, but the problem is, with 300 billion base pairs, that is still a long time in humans. So possibly a lot of players (multiple copies) are searching at once. Alternatively, a working hypothesis is histones, and the histone code simplify the searches by leaving only certain stretches of DNA exposed for the search, organizing areas of active and inactive chromatin, etc.

At the risk of making a fool of myself, let me handwave what I think is going on.

Referencing this paper...http://www.mat.puc.cl/~pasi2006/noterdoes.pdf

"Einstein's kinetic theory of the Brownian motion, based upon light water molecules continuously bombarding a heavy pollen, provided an explanation of diffusion from the Newtonian mechanics. Since the discovery of quantum mechanics it has been a challenge to verify the emergence of diffusion from the Schrodinger equation."

From a classical viewpoint, diffusion is the result of vibrating particles. As a guess, the simple view is that protein molecules sliding along DNA strands are vibrating very fast which provides both locomotion and binding site testing.

For some reason, I don't know for sure, the sliding protein molecule doesn't do a random walk, it goes in a single direction. However, I could envision some kind of latch preventing backwards movement which would convert the random vibration into forward movement only.

But Quantum Mechanics tells us there is no such thing as particles. Everything is a wavefunction. At this scale, the protein molecule could be in quantum superposition. From recent Quantum Biophysics discoveries, I will be biased and suggest it is practically a given. This would make this a super efficient search process.

Don’t be shy about suggesting I am a Quantum Quack, it won’t be the first time.

Meanwhile, to the point Dr. Hunter is trying to make with this thread…

"For some reason, I don't know for sure, the sliding protein molecule doesn't do a random walk, it goes in a single direction. However, I could envision some kind of latch preventing backwards movement which would convert the random vibration into forward movement only."

This depends on the protein. Some have been directly observed to do random walks (tether a fluorescent bead, or quantum dot, for example). Others (in the minority of ones I can think of) have 'molecular ratchets' that impart directionality. Imparting energy helps directionality, though some motors take some pretty random walks, too.

As for the quantum suggestion, I honestly don't know what on scale it might be discovered to apply (and I would challenge anyone who says the field does!). Proteins are big, yet we've got good evidence for electron tunneling across them.

Very recently, a example of quantum superposition of excited states was found to boost the efficiency of the photosynthetic machinery, for example:http://physicsworld.com/cws/article/news/41632

I don't have the exact words, but our lock-and-key descriptions of binding processes are probably desperately in need of better analogies.

"Yeah, this is quite complex."

Agreed. But too complex? There's the rub. And when we talk about "non-specific" DNA contacts-really that is just a couple of positive amino acids to interact with the phosphate backbone of DNA. A few arginines that put the sequence specific resides in a position to 'scan' is not really unimaginable, and the restriction from 3-d solution diffusion to linear diffusion would be a hell of an improvement in efficiency for selection.

These contacts, and the transition from non-specific to specific contacts have been imaged by X-ray crystallography, for example, here:

Transition from nonspecific to specific DNA interactions along the substrate-recognition pathway of dam methyltransferase.http://www.ncbi.nlm.nih.gov/pubmed/15882618

Oh, and the mathematical example is merely diffusion out of a 'box' of high concentration into low concentration 'bins'. That will observe a Gaussian distribution. Not really at all what we're talking about. Try Googling for something else.

You wrote..."As for the quantum suggestion, I honestly don't know what on scale it might be discovered to apply (and I would challenge anyone who says the field does!). Proteins are big, yet we've got good evidence for electron tunneling across them."

Thank you for the reply. I knew about the photosynthesis but I didn't know about the electron tunneling in electrons.

I just found this paper. It looks interesting...http://arxiv.org/PS_cache/arxiv/pdf/0907/0907.2494v1.pdf

"Had one asked a physicist twenty or even ten years ago if the human brain could exhibit quantum coherent phenomena, the response, after laughter, would have been that thermalization would have destroyed any vestige of quantum coherence, so the answer was ’No’.

It is therefore astonishing and important that recent results on the chlorophyll molecule, surrounded by its evolved ’antenna protein’, has been shown be quantum coherent for almost a nanosecond."..."The next fact of importance is that the cell is densely crowded with macromolecules. I do not know the distribution of distances between them, but it is on the order of dozens of angstroms, probably just enough to admit and coordinate the locations of one or more water molecule that then can support quantum coherent electron transport. This is open to investigation experimentally, including the effects of alteration of osmotic effects, swelling or shrinking cells by uptake or removal of water from the cells, on electron transport in cells. Such shrinkage or swelling could surpass the 9-14 angstrom separation needed for quantum coherent electron transport, hence be visible experimentally.

These facts raise the theoretical possibility that a percolating connected web of quantum coherent-decohering-recohering processes could form among and between the rich web of packed molecules in a cell, let alone its membrane surfaces. Hammeroff and Penrose (27) have suggested microtubules forming the cytoskeleton of cells as loci of coherent quantum behavior. Penrose, (8), has suggested that quantum gravity may play a role in the transition to classicity."

For those who don't know, Sir Roger Penrose is the mathematician who partnered with Steven Hawking to predict the existence of Black Holes.

Penrose argues against a materialist view of the mind. He teamed up with Dr. Hammeroff to create the Orchestrated Objective Reduction Model of Consciousness (Orch OR). Which involves microtubules.

The human brain is densely packed with microtubules. Just about every living thing has microtubules.

Robert, the tubulin dimer proteins that make up microtubules are bigger than the hOgg1 repair protein. If Penrose and Hameroff are right, it will mean a paradigm shift for a lot of people.

"If Penrose and Hameroff are right, it will mean a paradigm shift for a lot of people."

Sure. And we're open to it. This is why actual scientists laugh at the creationist strawman that portrays evolutionary biology as rigid and unchanging since the days of Darwin. Most of us are up for whatever mind-blowing discovery or paradigm shift is next. Sure, historically, some of the older ones get set in their ways. (Even the great ones-Einstein's dice come to mind). But if its scientific, explanatory, useful, and has evidence backing it, I'll give it a go, and I think most of my colleges feel the same.